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- PDB-12cj: Apo structure of dopamine-binding aptamer, DGR-1B -

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Basic information

Entry
Database: PDB / ID: 12cj
TitleApo structure of dopamine-binding aptamer, DGR-1B
ComponentsDGR-1B
KeywordsRNA / riboswitch / aptamer / dopamine / SELEX / L-DOPA
Function / homologySTRONTIUM ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsStelzig, D. / Hall, S.D. / Batey, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM152029 United States
CitationJournal: To Be Published
Title: Apo structure of dopamine-binding aptamer, DGR-1B
Authors: Stelzig, D. / Hall, S.D. / Batey, R.T.
History
DepositionMar 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DGR-1B
B: DGR-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,27529
Polymers49,9092
Non-polymers2,36627
Water32418
1
A: DGR-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,18115
Polymers24,9551
Non-polymers1,22714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DGR-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,09414
Polymers24,9551
Non-polymers1,13913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.764, 35.927, 97.279
Angle α, β, γ (deg.)90.000, 120.641, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11B-202-

HOH

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Components

#1: RNA chain DGR-1B


Mass: 24954.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Chemical...
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: Sr
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% v/v MPD, 20 mM spermine, 50 mM strontium chloride, 50 mM lithium chloride, 40 mM sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99992 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 2.93→43.94 Å / Num. obs: 10888 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.052 / Rrim(I) all: 0.139 / Net I/σ(I): 10.5
Reflection shellResolution: 2.93→3.01 Å / Rmerge(I) obs: 1.38 / Num. unique obs: 802 / CC1/2: 0.746 / Rpim(I) all: 0.544 / Rrim(I) all: 1.485

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→43.83 Å / SU ML: 0.1915 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1561 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248 475 4.37 %
Rwork0.2015 10392 -
obs0.2036 10867 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.77 Å2
Refinement stepCycle: LAST / Resolution: 2.93→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3304 27 18 3349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00183692
X-RAY DIFFRACTIONf_angle_d0.57765748
X-RAY DIFFRACTIONf_chiral_restr0.0285768
X-RAY DIFFRACTIONf_plane_restr0.0028154
X-RAY DIFFRACTIONf_dihedral_angle_d16.33191846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.340.30881390.27763377X-RAY DIFFRACTION97.4
3.34-4.210.26051670.20383437X-RAY DIFFRACTION99.83
4.21-43.830.21941690.17673578X-RAY DIFFRACTION99.89

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